AIDA group

PUBLICATION LIST

122. Chemical Modification of the siRNA Seed Region Suppresses Off-Target Effects by Steric Hindrance to Base-Pairing with Targets, Hanna Iribe, Kengo Miyamoto, Tomoko Takahashi, Yoshiaki Kobayashi, Jastina Leo, Misako Aida, and Kumiko Ui-Tei, ACS Omega, 2(5), 2055-2064 (2017).
DOI: 10.1021/acsomega.7b00291　

121. Hydration structure of trimethylamine N-oxide in aqueous solutions revealed by soft X-ray emission spectroscopy and chemometric analysis, Yuu Sasaki, Yuka Horikawa, Takashi Tokushim, Kazumasa Okada, Masaki Oura and Misako Aida, Physical Chemistry Chemical Physics, 18, 27648-27653 (2016).
DOI: 10.1039/C6CP03750J　

120. Quantifying Faculty Productivity in Japan: Development and Application of the Achievement-Motivated Key Performance Indicator, Misako Aida and Satoshi P. Watanabe, Research and Occasional Paper Series, CSHE 8.16, 2016,(October 2016).
URL: http://www.cshe.berkeley.edu/publications/quantifying-faculty-productivity-japan-development-and-application-achievement

119. Electronic origin of the dependence of hydrogen bond strengths on nearest-neighbor and next-nearest-neighbor hydrogen bonds in polyhedral water clusters (H2O)n, n = 8, 20 and 24, Suehiro Iwata, Dai Akase, Misako Aida and Sotiris S. Xantheas, Physical Chemistry Chemical Physics, 18, 19746-19756 (2016).
DOI: 10.1039/C6CP02487D　

118. Crosslinking reactions of 4-amino-6-oxo-2-vinylpyrimidine with guanine derivatives and structural analysis of the adducts, Shuhei Kusano, Shogo Ishiyama, Sik Lok Lam, Tsukasa Mashima, Masato Katahira, Kengo Miyamoto, Misako Aida and Fumi Nagatsugi, Nucleic Acids Research,, 43, 7717-7730 (2015).
DOI: 10.1093/nar/gkv797　

117. Reconsidering the activation entropy for anomerization of glucose and mannose in water studied by NMR spectroscopy, Ami Kosaka, Misako Aida, Yukiteru Katsumoto, Journal of Molecular Structure, 1093, 195-200 (2015).
DOI: 10.1016/j.molstruc.2015.03.038　

116. Synthesis and biological activities of the amide derivative of aplog-1, a simplified analog of aplysiatoxin with anti-proliferative and cytotoxic activities, Yusuke Hanaki, Ryo C. Yanagita, Takahiro Sugahara, Misako Aida, Harukuni Tokuda, Nobutaka Suzuki and Kazuhiro Irie, Bioscience, Biotechnology, and Biochemistry,, 79, 888-895 (2015).
DOI: 10.1080/09168451.2014.1002452　

115. Fundamental frequency from classical molecular dynamics, Tomonori Yamada and Misako Aida, Physical Chemistry Chemical Physics, 17, 3227-3240 (2015).
DOI: 10.1039/C4CP04068F　

114. A Comprehensive Search of Topologically Distinct Local Minimum Structures of Protonated Water Octamer and the Classification of O-H Topological Types, Dai Akase, Hiroyuki Teramae, Misako Aida, Chemical Physics Letters, 618, 51-56 (2015).
DOI: 10.1016/j.cplett.2014.10.071　

113. Distribution of Topologically Distinct Isomers of Water Clusters and Dipole Moments of Constituent Water Molecules at Finite Atmospheric Temperatures, Dai Akase, Misako Aida, Journal of Physical Chemistry A, 118(36), 7911-7924 (2014).
DOI: 10.1021/jp504854f　

112.Influence of Trimethylamine N-Oxide (TMAO) on the Three-dimensional Distribution and Alignment of Solvent Molecules in Aqueous Solution, Hideo Doi, Yudai Watanabe, Misako Aida, Chemistry Letters, 43(6), 865-867 (2014).
DOI: 10.1246/cl.140043　OPEN ACCESS PDF

111. A new variant of multicanonical Monte Carlo algorithm with specifying the temperature range and its application to the hydration free energy change of fluorinated methane derivatives, Hideo Doi, Misako Aida, Chemical Physics Letters, 595-596, 55-60 (2014).
DOI: 10.1016/j.cplett.2014.01.044

110. Helmholtz Energy Change between Neutral and Zwitterionic Forms of Glycine in Aqueous Solution Using Ab Initio Expanded QM/MM-MC with QM Solvent, Hidenori Miyamoto, Misako Aida, Chemistry Letters, 42(9), 1010-1012 (2013).
DOI: 10.1246/cl.130412　OPEN ACCESS PDF

109. Ab Initio QM/MM-MC Study on Hydrogen Transfer of Glycine Tautomerization in Aqueous Solution: Helmholtz Energy Changes along Water-mediated and Direct Processes, Hidenori Miyamoto, Misako Aida, Chemistry Letters, 42(6), 598-600 (2013).
DOI: 10.1246/cl.130126　OPEN ACCESS PDF

108. Macrodipole Moment of Polypeptides inβ-Sheet and Its Prediction from Dipole Moments of Amino Acid Residues as Building Blocks: Alanine and Glycine in β-Strand, Shunsuke Mieda, Misako Aida, Chemistry Letters, 42(5), 473-475 (2013).
DOI: 10.1246/cl.130084　OPEN ACCESS PDF

107. Hydration of Adamantane Skeleton: Water Assembling around Amantadine and Halo-substituted Adamantanes, Hideo Doi, Misako Aida, Chemistry Letters, 42(3), 292-294 (2013).
DOI: 10.1246/cl.2013.292　OPEN ACCESS PDF

106. Dipole Moments of Amino Acid Residues, Gly and Ala, in alpha-Helix: Quantum Chemical Building Blocks for Macrodipole Moment of alpha-Helical Polypeptide, Shunsuke Mieda, Misako Aida, Chemistry Letters, 41(12), 1579-1580 (2012).
DOI: 10.1246/cl.2012.1579

105.Digraphs in Chemistry: All Possible Structures and Temperature-Dependent Distribution of Water Clusters, Misako Aida, Dai Akase, Hideo Doi, Tomoki Yoshida, Practical Aspects of Computational Chemistry II: An Overview of the Last Two Decades and Current Trends,, pp.49-68,eds. Jerzy Leszczynski, Manoj K. Shukla, Springer Netherlands, 2012.
DOI: 10.1007/978-94-007-0923-2_3

104.“論文分析からみる広島大学の研究動向　−主として自然科学分野について −” 相田美砂子,吉田智喜, 大学論集, 43, pp.285-299, 2012年3月.
URL: http://ir.lib.hiroshima-u.ac.jp/00033160
本文: DaigakuRonshu_43_285.pdf

103. Solvent distributions, solvent orientations and specific hydration regions around 1-adamantyl chloride and adamantane in aqueous solution, Masayuki Ohisa, Misako Aida, Chemical Physics Letters, 511(1-3), 62 (2011).
DOI: 10.1016/j.cplett.2011.06.020

102. Self-assembled monolayers of cyanoterphenyl terminated alkyl disulfides studied by vibrationally and electronically doubly-resonant sum-frequency generation spectroscopy, Tetsuhiko Nagahara, Hitoshi Fukushima, Misako Aida and Taka-aki Ishibashi, Chemical Physics Letters, 506, 190-195 (2011).
DOI: 10.1016/j.cplett.2011.03.019

101. Structures of Molecules in Ground and Excited Vibrational States from Quasiclassical Direct ab Initio Molecular Dynamics, T. Yamada and M. Aida Journal of Physical Chemistry A, 114(21), 6273-6283 (2010).
DOI: 10.1021/jp912269v

100. Self-Assembled Monolayers of Double-Chain Disulfides of Adenine on Au: An IR-UV Sum-Frequency Generation Spectroscopic Study, T.Nagahara, T. Suemasu, M. Aida and T. Ishibashi, Langmuir,, 26, 389-396 (2010).
DOI: 10.1021/la9021992

99. 実数値GAを用いた薬物標的GPCRの活性型立体構造の探索, 石野洋子, 原田隆範, 相田美砂子 人工知能学会論文誌, 24(5), 386-396 (2009).
DOI: 10.1527/tjsai.24.386

98. ONIOM Study of the Mechanism of the Enzymatic Hydrolysis of Biodegradable Plastics, Y. Sakae, T. Matsubara, M. Aida, H. Kondo, K. Masaki, and H. Iefuji Bulletin of the Chemical Society of Japan, 82(2), 338-346 (2009).
DOI: 10.1246/bcsj.82.338

97. Classification of OH Bonds and Infrared Spectra of the Topology-Distinct Protonated Water Clusters H3O+(H2O)n-1 (n <= 7), Maihemutijiang Jieli, and Misako Aida, J. Phys. Chem. A, 113(8), 1586-1594 (2009).
DOI: 10.1021/jp810735m

96. Chiral Sum Frequency Spectroscopy of Thin Films of Porphyrin J-Aggregates, T. Nagahara, K. Kisoda, H. Harima, M. Aida, T. Ishibashi, Journal of Physical Chemistry B,, 113(15), 5098-5103 (2009).

95. Identification of chemical species of fluorescein isothiocyanate isomer-I (FITC) monolayers on platinum by doubly resonant sum-frequency generation spectroscopy, T. Maeda, T. Nagahara, M. Aida, T. Ishibashi, J. Raman Spectrosc.,, 39(11), 1694-1702 (2008).

94. A Theoretical Insight into the Interaction of Fatty Acids Involved in Royal Jelly with the Human Estrogen Receptor β, Toshiaki Matsubara, Hiroyuki Sugimoto and Misako Aida, Bulletin of the Chemical Society of Japan, 81(10), 1258-1266 (2008).
DOI: 10.1246/bcsj.81.1258

93. Thermally induced double proton transfer in GG and wobble GT base pairs: A possible origin of the mutagenic guanine, Adchara Padermshoke, Yukiteru Katsumoto, Ryuta Masaki and Misako Aida, Chemical Physics Letters, 457(1-3), 232-236 (2008).
DOI: 10.1016/j.cplett.2008.04.029

92. Fundamental absorption frequencies and mean structures at vibrational ground state from quasi-classical direct ab initio MD: Triatomic molecule, Tomonori Yamada, Misako Aida, Chemical Physics Letters, 452(4-6), 315-320 (2008).
DOI: 10.1016/j.cplett.2007.12.055

91. Two-dimensional free-energy surface on the exchange reaction of alkyl chloride/chloride using the QM/MM-MC method, Masayuki Ohisa, Hiroshi Yamataka, Michel Dupuis and Misako Aida, Physical Chemistry Chemical Physics, 10, 844-849 (2008).
DOI: 10.1039/b712565h

90. An Insight into the Environmental Effects of the Pocket of the Active Site of the Enzyme. Ab initio ONIOM-Molecular Dynamics (MD) Study on Cytosine, Toshiaki Matsubara, Michel Dupuis, and Misako Aida Journal of the Computational Chemistry, 80(29), 458-465 (2008).
DOI: 10.1002/jcc.20805

89. Enumeration of Topology-Distinct Structures and Possible Stable Structures of Protonated Water Clusters, H₃O⁺(H₂O)_n−1 (n≤5), Maihemutijiang Jieli, Toshiko Miyake and Misako Aida, Bulletin of the Chemical Society of Japan, 80(11), 2131-2136 (2007).
DOI: 10.1246/bcsj.80.2131

88. Kinetic Investigations of the Process of Encapsulation of Small Hydrocarbons into a Cavitand-Porphyrin, Jun Nakazawa, Yoshitake Sakae, Misako Aida, and Yoshinori Naruta, Journal of Organic Chemistry, 72(25), 9448-9455 (2007).
DOI: 10.1021/jo701299v

87. Ab initio ONIOM-Molecular dynamics (MD) study on the deamination reaction by cytidine deaminase, Toshiaki. Matsubara, Michel Dupuis and Misako Aida, Journal of Physical Chemistry B, 111, 9965-9974 (2007).
DOI: 10.1021/jp072732k

86. Electronic states of the DNA polynucleotides poly(dG)-poly(dC) in the presence of iodine, Masashi Furukawa, Hiroyuki S. Kato, Masateru Taniguchi, Tomoji Kawai, Takaki Hatsui, Nobuhiro Kosugi, Tomoki Yoshida, Misako Aida, and Maki Kawai, Physical Review B, 75, 045119 (2007).
DOI: 10.1103/PhysRevB.75.045119

85. The ONIOM molecular dynamics method for biochemical applications:cytidine deaminase, Toshiaki Matsubara, Michel Dupuis and Misako Aida, Chemical Physics Letters, 437(1-3), 138-142 (2007).
DOI: 10.1016/j.cplett.2007.01.085

84. Photochemistry of 2-(methylamino)pyridine in a low-temperature argon matrix: Amino-imino tautomerism and rotational isomerism, Nobuyuki Akai, Keiichi Ohno and Misako Aida, Journal of Photochemistry and Photobiology A: Chemistry, 187, 113-118(2007).
DOI: 10.1016/j.jphotochem.2006.10.002

83. BSSE-corrected Three-body Interaction Energy in the Recognition of GC Base Pair by Asparagine, Tomoki Yoshida and Misako Aida, Chemistry Letters, 36(1), 124-125(2007).
DOI: 10.1246/cl.2007.124

82. Dimerization and Double Proton Transfer-Induced Tautomerism of 4(3H) -Pyrimidinone in Solution Studied by IR Spectroscopy and Quantum Chemical Calculations, Adchara Padermshoke, Yukiteru Katsumoto and Misako Aida, Journal of Physical Chemistry B, 110, 26388-26395 (2006).
DOI: 10.1021/jp065408i

81. Population of 6-Enol Form is Higher in 8-Oxoguanine than in Guanine, Tomoki Yoshida and Misako Aida, Chemistry Letters, 35(8), 924-925(2006).
DOI: 10.1246/cl.2006.924

80. H-bond patterns and structure distributions of water octamer (H₂O)₈ at finite temperatures, Toshiko Miyake and Misako Aida, Chemical Physics Letters, 427, 215-220 (2006).
DOI: 10.1016/j.cplett.2006.06.077

79. Photoinduced Amino-Imino Tautomerism: An Infrared Study of 2-Amino-5-methylpyridine in a Low-Temperature Argon Matrix JPCA, Nobuyuki Akai, Takanori Harada, Kei Shin-ya, Keiichi Ohno and Misako Aida, Journal of Physical Chemistry, A110(18), 6016-6022 (2006).
DOI: 10.1021/jp056290t

78. A Quantum Chemical Study of the Catalysis for Cytidine Deaminase:Contribution of the Extra Water Molecule, Toshiaki Matsubara, Masashi Ishikura, Misako Aida, Journal of Chemical Information and Modeling, 46(3), 1276-1285 (2006).
DOI: 10.1021/ci050479k

77. Quantum Chemical Study of the Interaction of the Short-Chain Poly(oxyethylene)s CH₃(OCH₂CH₂)mOCH₃ (C₁E_mC₁; m=1 and 2) with a Water Molecule in the Gas Phase and the Solutions, Shaheda A. Wahab, Takanori Harada, Toshiaki Matsubara and Misako Aida, Journal of Physical Chemistry A, 110(3), 1052-1059 (2006).
DOI: 10.1021/jp055054f

76. Ab initio MO and quasi-classical direct ab initio MD studies on the nitrogen inversion of trimethylamine, Masato Tanaka and Misako Aida, Chemical Physics Letters, 417, 316-319 (2006).
DOI: 10.1016/j.cplett.2005.10.014

75. Vibrational anharmonicity of acetic acid studied by matrix-isolation near-infrared spectroscopy and DFT calculation, Nobuyuki Akai, Yukiteru Katsumoto, Keiichi Ohno and Misako Aida, Chemical Physics Letters, 413, 367-372 (2005).
DOI: 10.1016/j.cplett.2005.08.013

74. Photoinduced amino-imino tautomerism of 2-aminopyridine in a low-temperature argon matrix, Nobuyuki Akai, Keiichi Ohno and Misako Aida, Chemical Physics Letters, 413, 306-310 (2005).
DOI: 10.1016/j.cplett.2005.07.101

73. Photochemistry of p-toluidine in a low-temperature argon matrix. Infrared spectrum and geometrical structure of 4-methylanilino radical, Nobuyuki Akai, Hiroshi Yoshida, Keiichi Ohno and Misako Aida, Chemical Physics Letters, 403, 390-395 (2005).
DOI: 10.1016/j.cplett.2005.01.046

72. Fundamental absorption frequency from quasi-classical direct ab initio molecular dynamics: Diatomic Molecule, Misako Aida and Michel Dupuis, Chemical Physics Letters, 401, 170-174 (2005).
DOI: 10.1016/j.cplett.2004.11.046

71. An Ab Initio MO Study on Orbital Interaction and Charge Distribution in Alkali Metal Aqueous Solution: Li⁺, Na⁺ and K⁺, Masato Tanaka and Misako Aida, Journal of Solution Chemistry, 33 (6-7), 887-901(2004).
DOI: 10.1023/B:JOSL.0000043648.89461.62

70. Protonation-induced Conformational Changes of 2-(N,N-Dimethylamino)ethanethiol. Importance of Strong N-H⁺...S and N-H⁺...S- Hydrogen Bonding, Keiichi Ohno, Shingo Matsumoto, Misako Aida, and Hiroatsu Matsuura, Chemistry Letters, 32(9), 828-829 (2003).
DOI: 10.1246/cl.2003.828

69. IR and Raman Intensities in Vibrational Spectra from Direct Ab Initio Molecular Dynamics: D₂O as an Illustration, Misako Aida and Michel Dupuis, Journal of Molecular Structure (Theochem), 633, 247-255 (2003).
DOI: 10.1016/S0166-1280(03)00280-X

68. Dynamics-Driven Reaction Pathway in an Intrameolecular Rearrangement, Salai Cheettu Ammal, Hiroshi Yamataka, Misako Aida and Michel Dupuis, Science, 299, 1555-1557 (2003).
DOI: 10.1126/science.1079491

67. Ab initio molecular dynamics studies on substitution vs. electron transfer reactions of substituted ketyl radical anions with chloroalkanes: How do the two products form in a borderline mechanism?, Hiroshi Yamataka, Misako Aida and Michel Dupuis, Journal of Physical Organic Chemistry, 16, 475-483 (2003).
DOI: 10.1002/poc.610

66. Hydrogen Bonding Patterns in Water Clusters: Trimer, Tetramer and Pentamer, Toshiko Miyake and Misako Aida, Internet Electronic Journal of Molecular Design, 2, 24-32 (2003). http://biochempress.com/Files/iejmd_2003_2_0024.pdf

65. Enumeration of topology-distinct structures of hydrogen bonded water clusters, Toshiko Miyake and Misako Aida, Chemical Physics Letters, 363, 106-110 (2002).
DOI: 10.1016/S0009-2614(02)01150-8

64. Ab Initio Direct Molecular Dynamics Simulations and QM/MM Computations in Search of Organic Reaction Mechanism, Hiroshi Yamataka and Misako Aida, Bulletin of the Chemical Society of Japan, 75, 2555-2569 (2002).
DOI: 10.1246/bcsj.75.2555

63.A polarizable mixed Hamiltonian model of electronic structure for micro-solvated excited states. I. Energy and gradients formulation and application to formaldehyde (¹A₂), Michel Dupuis, Misako Aida, Y. Kawashima and Kimihiko Hirao, Journal of Chemical Physics, 117 (3), 1242-1255 (2002).
DOI: 10.1063/1.1483858

62.Analysis of borderline substitution/electron-transfer pathways from direct ab initio MD simulations, Hiroshi Yamataka, Misako Aida and Michel Dupuis, Chemical Physics Letters, 353, 310-316 (2002).
DOI: 10.1016/S0009-2614(02)00041-6

61.Evaluation of free energy landscape for base-amino acid interactions using ab initio force field and extensive sampling, Tomoki Yoshida, Tomohiro Nishimura, Misako Aida, Fabio Pichierri, Michael M. Gromiha and Akinori Sarai, Biopolymers, 61, 84-95 (2001/2002).
DOI: 10.1002/bip.10045

60.Modeling of reactivities of organic molecules by means of ab initio MD method, Misako Aida, Hiroshi Yamataka and Michel Dupuis, Large-Scale Scientific Computations of Engineering and Environmental Problems II, pp.319-327, eds. Michael Griebel, Svetozar Margenov and Plamen Yalamov, Vieweg, Braunschweig/Wiesbaden, 2000.

59.Critical Assessment of the Hybrid QM/MM-pol-vib Approach: Small water clusters using polarizable flexible water potentials, Misako Aida, Hiroshi Yamataka and Michel Dupuis, International Journal of Quantum Chemistry, 77, 199-210 (2000).
DOI: 10.1002/(SICI)1097-461X(2000)77:1<199::AID-QUA19>3.0.CO;2-T

58.Free-energy maps of base-amino acid interactions for DNA-protein recognition, Fabio Pichierre, Misako Aida, M. Michael Gromiha and Akinori Sarai, Journal of the American Chemical Society, 121, 6152-6157 (1999).
DOI: 10.1021/ja984124b

57.Raman spectrum of [5'-¹³C]thymidine: vibrations of its 5'-end atomic group, Masamichi Tsuboi, Yukinori Takeuchi, Etsuko Kawashima, Yoshiharu Ishido and Misako Aida, Spectrochimica Acta, A55, 1887-1896 (1999).
DOI: 10.1016/S1386-1425(99)00048-7

56.One transition state leading to two product states: ab initio MD simulations of the reaction of formaldehyde radical anion and methyl chloride, Hiroshi Yamataka, Misako Aida and Michel Dupuis, Chemical Physics Letters, 300, 583-587 (1999).
DOI: 10.1016/S0009-2614(98)01440-7

55.Radiation-induced DNA damage and repair: an approach from ab initio MO method, Misako Aida, Motohisa Kaneko and Michel Dupuis, Computational Molecular Biology, pp.211-243, ed. J. Leszczynski, Elsevier, Netherlands, 1999.

54.Determination of the Three-Dimensional Structure of Crystalline Leu-Enkephalin Dihydrate Based on Six Sets of Accurately Determined Interatomic Distances from ¹³C-REDOR NMR and the Conformation-Dependent ¹³C Chemical Shift, Katsuyuki Nishimura, Akira Naito, Satoru Tuzi, Hazime Saito, Chikao Hashimoto and Misako Aida, Journal of Physical Chemistry, B102(38), 7476-7483 (1998).
DOI: 10.1021/jp981683w

53.Ab initio MD simulations of a prototype of methyl chloride hydrolysis with explicit consideration of three water molecules: a comparison of MD trajectories with the IRC path, Misako Aida, Hiroshi Yamataka and Michel Dupuis, Theoretical Chemistry Accounts, 102, 262-271 (1999).
DOI: 10.1007/s002140050497

52.An ab initio MO study on the hydrolysis of methyl chloride, Hiroshi Yamataka and Misako Aida, Journal of Molecular Structure (Theochem), 461-462, 417- 427 (1999).

51.Ab initio molecular dynamics simulations on the hydrolysis of methyl chloride with explicit consideration of three water molecules, Misako Aida, Hiroshi Yamataka and Michel Dupuis, Chemical Physics Letters, 292, 474-480 (1998).
DOI: 10.1016/S0009-2614(98)00706-4

50.An ab initio MO study on the hydrolysis of methyl chloride with explicit consideration of 13 water molecules, Hiroshi Yamataka and Misako Aida, Chemical Physics Letters, 289, 105-109 (1998).
DOI: 10.1016/S0009-2614(98)00311-X

49.Synthesis of novel dioxane nucleosides having two bases, physico-chemical properties, and their biological activities, Naoko Kajimoto, Jiro Yamaizumi, Misako Aida, Kazuho Harada and Mitsuaki Maeda, Nucleic Acids Symposium Series, No.37, 5-6 (1997).

48.Electronic structure near the Fermi level and STM images of Pd(110) c(4x2)-benzene, Jun Yoshinobu, Maki Kawai, Issei Imamura, Fumiyuki Marumo, Ryochi Suzuki, Hiroyuki Ozaki, Masaru Aoki, Shigeru Masuda, Shin-ichiro Tanaka, Masao Kamada and Misako Aida, Journal of Electron Spectroscopy and Related Phenomina, 88-91, 997-1002 (1998).
DOI: 10.1016/S0368-2048(97)00115-1

47.An ab initio MO study on fragmentation reaction mechanism of thymine dimer radical cation, Misako Aida, Fukiko Inoue, Motohisa Kaneko and Michel Dupuis, Journal of the American Chemical Society, 119, 12274-12279 (1997).
DOI: 10.1021/ja970184q

46.Raman Scattering Tensors of Tyrosine, Masamichi Tsuboi, Yoshiko Ezaki, Misako Aida, Mika Suzuki, Abliz Yumit, Koichi Ushizawa and Toyotoshi Ueda, Biospectroscopy, 4, 61-71 (1998).
DOI: 10.1002/(SICI)1520-6343(1998)4:1<61::AID-BSPY7>3.0.CO;2-V

45.Direct observation of molecule-substrate antibonding states near Fermi level in Pd(110) c(4x2)-benzene, Jun Yoshinobu, Maki Kawai, Issei Imamura, Fumiyuki Marumo, Ryochi Suzuki, Hiroyuki Ozaki, Masaru Aoki, Shigeru Masuda and Misako Aida, Physical Review Letters, 79, 3942-3945 (1997).
DOI: 10.1103/PhysRevLett.79.3942

44.Free radical chemistry of cigarette smoke and its implication in human cancer, M.Kodama, M.Kaneko, M.Aida, F.Inoue, T.Nakayama and H.Akimoto, Anticancer Research, 17, 433-438 (1997).

43.Raman scattering tensors in thymine molecule from an ab initio MO calculation, Masamichi Tsuboi, Akiko Kumakura, Misako Aida, Motohisa Kaneko, Michel Dupuis, Koichi Ushizawa and Toyotoshi Ueda, Spectrochimica Acta, A53, 409-419 (1997).
DOI: 10.1016/S1386-1425(96)01812-4

42.Vibrational modes in thymine molecule from an ab initio MO calculation, Misako Aida, Motohisa Kaneko, Michel Dupuis, Toyotoshi Ueda, Koichi Ushizawa, Gen Ito, Akiko Kumakura and Masamichi Tsuboi, Spectrochimica Acta, A53, 393-407 (1997).
DOI: 10.1016/S1386-1425(96)01811-2

41.Derivation and assessment of a new set of ab initio potentials and its application to molecular dynamics simulations of biological molecules in vacuo, in crystal and in aqueous solution, Misako Aida, Computational Chemistry: Reviews of Current Trends Vol.2, pp.217-250, ed. J. Leszczynski, World Scientific Publishing, Singapore, 1997.

40.Microscopic Observation of Molecules in Adsorption and Reaction on Metal Surfaces: Benzene on Pd(110), Jun Yoshinobu, Maki Kawai, Issei Imamura, Fumiyuki Marumo, Misako Aida, Hiroyuki Tanaka and Tomoji Kawai, Proceedings of Oji Seminar on Chemical Processes at Surface based on Atomic Scale Structure and Dynamics, pp. 112-115, ed. K. Tanaka, 1996.

39.Determination of the Three-dimensional Structure of a New Crystalline Form of N-Acetyl-Pro-Gly-Phe As Revealed by ¹³C-REDOR, X-Ray Diffraction, and Molecular Dynamics Calculation, Akira Naito, Katsuyuki Nishimura, Shigeki Kimura, Satoru Tuzi, Misako Aida, Noritake Yasuoka, and Hazime Saito, Journal of Physical Chemistry, 100, 14995 - 15004 (1996).
DOI: 10.1021/jp960179t

38.Molecular Dynamics Simulations of a Simple Tripeptide, N-acetyl-Pro-Gly-Phe in the Crystalline States: Distinction of the -turn Type I from the Type II form, Misako Aida, Akira Naito and Hazime Saito, Journal of Molecular Structure (Theochem), 388, 187-200 (1996).
DOI: 10.1016/S0166-1280(96)80032-7

37.An ab initio MO study on thymine dimer and its radical cation, Misako Aida, Motohisa Kaneko and Michel Dupuis, International Journal of Quantum Chemistry, 57, 949-957 (1996).
DOI: 10.1002/(SICI)1097-461X(1996)57:5<949::AID-QUA15>3.0.CO;2-S

36.Structural Fluctuation of Methyl N,N'-diacetyl--D-Chitobioside in vacuo and in Aqueous Solution: Molecular Dynamics Simulations and Proton NMR Spectroscopy, Misako Aida, Yoko Sugawara, Setsuko Oikawa and Kimiko Umemoto, International Journal of Biological Macromolecules, 17, 227-235 (1995).
DOI: 10.1016/0141-8130(95)92690-R

35.Theoretical studies on specific interactions between biological molecules: Interaction of cationic arginine with anionic glutamic acid, Misako Aida, Journal of Molecular Structure (Theochem), 311, 45-53 (1994).

34.Theoretical Studies on Hydrogen Bonding Interactions between Peptide Units, Misako Aida, Bulletin of the Chemical Society of Japan, 66, 3423-3429 (1993).
DOI: 10.1246/bcsj.66.3423

33.Ab initio force field for simulations of proteins and nucleic acids: Application to molecular dynamics simulations in aqueous solution, Giogina Corongiu and Enrico Clementi, Computer Aided Innovation of New Materials II, eds. Misako Aida, M. Doyama, J. Kihara, M. Tanaka and R. Yamamoto, Elsevier Science Publishers, Amsterdam, 1181-1184, (1993).

32.Ab Initio Force Field for Simulations in Aqueous Solution of Biological Molecules, Misako Aida, Giogina Corongiu and Enrico Clementi, Proceedings of the International Symposium on Advanced Computing forLife-Science, 61-63, eds. M. Okamoto and K. Shimizu, 1992.

31.Molecular dynamics simulations with ab initio interaction potentials, G. Corongiu, M. Aida, M.F. Pas and E. Clementi, Modern Techniques in Computational Chemistry: MOTECC-91, chapter 21, 847-919, ed. E. Clementi, ESCOM Science Publishers, Leiden, 1991.

30.Ab initio force field for simulations of proteins and nucleic acids, Misako Aida, Giorgina Corongiu and Enrico Clementi, International Journal of Quantum Chemistry, 42, 1353-1381 (1992).
DOI: 10.1002/qua.560420514

29.Molecular dynamics simulation in vacuo and in solution of Cyclolinopeptide A: A conformational study, Michele Saviano, Misako Aida and Giorgina Corongiu, Biopolymers, 31, 1017-1024, 1991.
DOI: 10.1002/bip.360310811

28.Monte Carlo and molecular dynamics simulations, E. Clementi, G. Corongiu, M. Aida, U. Neisar and G. Kneller, Modern Techniques in Computational Chemistry: MOTECC-90, chapter 17, 805-888, ed. E. Clementi, ESCOM Science Publishers, Leiden, 1990.

27.Intermolecular nuclear overhauser effect and atomic pair potential approaches to wheat germ agglutinin - sugar binding, K. Umemoto, S. Oikawa, M. Aida and Y. Sugawara, Journal of Biomolecular Structure & Dynamics, 6, 593-608, 1988.

26.Ab initio molecular orbital study of the mispairing ability of a nucleotide base analogue, N⁴-aminocytosine, Misako Aida, Kazuo Negishi, Hikoya Hayatsu and Mitsuaki Maeda, Biochemical and Biophysical Research Communications, 153, 552-557, 1988.

25.Molecular orbital studies of the action of thyroid hormone analogs:effects on oxygen consumption of mitochondria and horseradish peroxidase-catalyzed NADH oxidation, Junji Sakurada, Misako Aida, Chikayoshi Nagata and Toichiro Hosoya, Journal of Biological Physics, 16, 17-23, 1988.
DOI: 10.1007/BF01861087

24.¹³C NMR spectra of para-substituted methoxybenzenes and phenols in the solid state: Examination of chemical shift non-ezuivalence in ortho and meta carbons related to non-ezuivalent electron distibution, and application to assignment of peaks in meso-hexestrol and its derivatives, Hazime Saito, Motoko Yokoi, Misako Aida, Masahiko Kodama, Taiko Oda and Yoshihiro Sato, Magnetic Resonance in Chemistry, 26, 155-161, 1988.
DOI: 10.1002/mrc.1260260212

23.Ab initio molecular orbital study on the pairing and stacking interactions between nucleic acid bases in relation to the biological activities, Chikayoshi Nagata and Misako Aida, Journal of Molecular Sturcture (THEOCHEM), 179, 451-466, 1988.
DOI: 10.1016/0166-1280(88)80141-6

22.Synthesis and properties of purinophanes: Relationship between the magnitude of hypochromism and stacking geometry of purine rings, F. Seyama, K. Akahori, H. Sakata, S. Misumi, M. Aida and C. Nagata, Journal of the American Chemical Society, 110, 2192-2201, 1988.
DOI: 10.1021/ja00215a032

21.An ab initio molecular orbital study on the sequence-dependency of DNA conformation: an evaluation of intra- and inter-strand stacking interaction energy, Misako Aida, Journal of theoretical Biology, 130, 327-335, 1988.
DOI: 10.1016/S0022-5193(88)80032-8

20.Characteristics of the Watson-Crick type hydrogen-bonded DNA base pairs: an ab initio molecular orbital study, Misako Aida, Journal of Computational Chemistry, 9, 362-368, 1988.
DOI: 10.1002/jcc.540090411

19.Reaction of 5-trifluoromethyl-2-deoxyuridine and 1-methyl-5-trifluoromethyluracil with methoxyamine: model studies for the interaction between thymidylate synthetase and 5-trifluoromethyl-2-deoxyuridine 5-phosphate, Yusuke Wataya, Yumi Sonobe, Mitsuaki Maeda, Ziro Yamaizumi, Misako Aida and Daniel V. Santi, Journal of Chemical Society Perkin Transactions I, 2141-2147, 1987.
DOI: 10.1039/P19870002141

18.An ab initio molecular orbital study on the characteristics of 8-hydroxyguanine, Misako Aida and Susumu Nishimura, Mutation Research, 192, 83-89, 1987.

17.Analysis of the -electronic structure of infinitely large networks. I. Some remarks on the characteristic polynomial and density of states of large polycyclic aromatic hydrocarbons, Haruo Hosoya, Misako Aida, Reiko Kumagai and Kazu Watanabe, Journal of Computational Chemistry, 8, 358-366, 1987.
DOI: 10.1002/jcc.540080412

16.Tables of the non-adjacent number, topological index, and characteristic polynomials of heptahex graphs, Haruo Hosoya, Atsuko Uchiyama, Misa Kadota, Taneko Chida, Misako Aida and Tamie Yamaguchi, Natural Science Report of the Ochanomizu University, 37, 133-168, 1986.

15. A high-resolution solid-state ²³Na NMR study of sodium complexes with solvents, small ligand molecules, and ionophores. ²³Na chemical shifts as means for identification and characterization of ion-ion, ion-solvent, and ion-ligand interactions, Ryoko Tabeta, Misako Aida and Hazime Saito, Bulletin of the Chemical Society of Japan, 59, 1957-1966, 1986.
DOI: 10.1246/bcsj.59.1957

14.An ab initio MO study on the disulfide bond: properties concerning the characteristic S-S dihedral angle, Misako Aida and Chikayoshi Nagata, Theoretica Chimica Acta, 70, 73-80, 1986.
DOI: 10.1007/BF00532204

13.An ab initio molecular orbital study on the stacking interaction between nucleic acid bases: Dependence on the sequence and relation to the conformation, Misako Aida and Chikayoshi Nagata, International Journal of Quantum Chemistry, 29, 1253-1261, 1986.
DOI: 10.1002/qua.560290522

12.An explanation of the induction of mutations by 2-aminopurine from an ab initio molecular orbital study, Misako Aida, Kazumasa Yamane and Chikayoshi Nagata, Mutation Research, 173, 49-54, 1986.
DOI: 10.1016/0165-7992(86)90010-2

11.Pairing and stacking interactions between nucleic acid bases in relation to the biological functions of nucleic acids, Chikayoshi Nagata and Misako Aida, Biomolecules: electronic aspects, 91-104, eds. C. Nagata, M. Hatano, J. Tanaka and H. Suzuki, Japan Scientific Societies Press, Tokyo / Elesevier, Amsterdam, 1985.

10.Ab initio molecular orbital study on the mechanism of the Haber-Weiss reaction, Chikayoshi Nagata and Misako Aida, Journal of Biological Physics, 12, 39-43, 1984.
DOI: 10.1007/BF01858251

9.Ab initio molecular orbital study of the interaction of Li⁺, Na⁺ and K⁺ with the pore components of ion channels: Consideration of the size, structure and selectivity of the pore of the channels, Chikayoshi Nagata and Misako Aida, Journal of theoretical Biology, 110, 569-585, 1984.
DOI: 10.1016/S0022-5193(84)80146-0

8.An ab initio MO study on the thiol-disulphide exchange reaction, Misako Aida and Chikayoshi Nagata, Chemical Physics Letters, 112, 129-132, 1984.
DOI: 10.1016/0009-2614(84)85006-X

7.An electron spin resonance study on the free radicals produced from aclacinomycin A and its derivatives: Analysis of hyperfine structure of the spectra by means of molecular orbital method, Masahiko Kodama, Misako Aida, Chikayoshi Nagata, Toshikazu Oki and Yasue Matsuzawa, Cancer Biochemistry Biophysics, 6, 243-247, 1983.

6.Ab initio molecular orbital study on the thermostability of the extreme thermophile tRNA: role of the base stacking, Misako Aida, Chikayoshi Nagata, Iwao Ohmine and Keiji Morokuma, Journal of theoretical Biology, 99, 599-608, 1982.
DOI: 10.1016/0022-5193(82)90213-2

5.Why O⁶-alkylguanine is specifically promutagenic? Ab initio molecular orbital consideration, Chikayoshi Nagata, Eriko Takeda and Misako Aida, Mutation Research, 105, 1-8, 1982.
DOI: 10.1016/0165-7992(82)90199-3

4.Structure and hypochromism of (6,9)(9',6') purinophanes, Fumio Hama, Yoshiteru Sataka, Soichi Misumi, Misako Aida and Chikayoshi Nagata, Tetrahedron Letters, 23, 3061-3064, 1982.
DOI: 10.1016/S0040-4039(00)87533-4

3.Ab initio MO study on base stacking: adenine - adenine interaction in single-stranded polyadenylic acid (poly A), Misako Aida and Chikayoshi Nagata, Chemical Physics Letters, 86, 44-46, 1982.
DOI: 10.1016/0009-2614(82)83113-8

2.Metabolically generated free radicals from many types of chemical carcinogens and binding of the radicals with nucleic acid bases, Chikayoshi Nagata, Masahiko Kodama, Teruyuki Kimura and Misako Aida, The Jerusalem Symposia on Quantum Chemistry and Biochemistry, 13 Carcinogenesis: Fundamental Mechanisms and Environmental Effects, 43-54, eds. B. Pullman, P.O.P. Ts'O and H. Gelboin, Reidel, 1980.

1.MO- and VB- benzene characters. Analysis of the "Clar's aromatic sextet" in polycyclic aromatic hydrocarbons, Misako Aida and Haruo Hosoya, Tetrahedron, 36, 1317-1326, 1980.
DOI: 10.1016/0040-4020(80)85043-5